Questions tagged [phylogenetics]

A sub-discipline of evolutionary biology which involves the study of evolutionary relatedness between different organisms based on their molecular and morphological features.

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87 views

On the origin and evolution of vaccinia virus

I was browsing Wikipedia and learned that vaccinia virus, the basis of the smallpox (variola virus) vaccine, was originally thought to be derived from cowpox but was later discovered to be a separate ...
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Why Account for Phylogeny when using Relative Brain Size as a Surragate for Intelligence

This paper tries to relate intelligence, life history, and urban fitness of birds. They use relative brain size of each species as a surrogate measure of intelligence. Although this may not be the ...
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How old is the Pogona genus?

What it says on the title, how old is the genus Pogona, which includes all bearded dragons? I tried looking online, and all I got was the useless answer of “bearded dragons are descended from their ...
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What are the branches in the phenogram?

Do you also consider the branch before the node as a branch? Or do you only consider the branches that are connected to leaf?
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248 views

Defining "species" (Are species an emergent property or an ensemble of quantitative differences?)

Interbreeding Defining species by the criteria of not being able to breed is problematic: The concept loses its meaning in phylogenetic prospective, since closely related species were able to breed ...
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Blood samples in cell lysis

I will be joining a team of field biologists on a trip to some uninhabited islands in the tropics. We will be collecting bird blood samples for some genetic research. We will be out there for two ...
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Is the General Cirrate Octopus Form the Basalmost Octopoda Morphology?

The reason I ask this is due to the distinctive internal mantle shells of cirrina, of which the incerrata have stylets that are a remnant of the cirrate shell. Along with this, both cirrate octopuses ...
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Creating a phylogenetic tree from my selected publicly-available sequences (WGS) in NCBI

I'm currently writing a paper on the comparison of virulence genes for a group of bacteria. I got my data from publicly-available whole genome sequences in NCBI. Now, I want to create a phylogenetic ...
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Advice on type of database and software for research on genetic diversity of crops

for a research project I am evaluating the potential of Robusta coffee genetic resources in the tropic region of Africa. Different ex-situ genetic lines will be mapped as well as chemical, ...
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Which is the best model organism to implement an evolutionary study for P.falciparum?

I have to study and implement some evolutionary statistics for P.falciparum. In your opinion and by your experience, which organism should I consider in order to take the orthologs to implement this ...
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Why is the null hypothesis of trait evolution Brownian motion?

Many models of continuous trait evolution assume that traits evolve according to Brownian motion. What is the biological or physical basis for this choice? I realize there are models that do not ...
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how to estimate phylogeny without using DNA sequences?

I am new to bioinformatics, I am reading ‘Analysis of Phylogenetics Second Edition and Evolution with R’ from Emmanuel Paradis. I can create phylogeny from DNA sequences, by first calculating the ...
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Examples of species whose extinct common ancestor is well documented?

If we follow the ascendence line of two closely related species we can build a "Theoretical" common ancestor, whose characteristics were inherited with few differences by the offspring. <...
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Metrics to analyze branch lengths in phylogenetic trees

I'm interested know about some basic metrics that could be used to discriminate trees based on their branch lengths. I know of branch length unaware topological/tree shape-based methods such as ...
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55 views

Controlling for phylogenetic signal - what is statistically appropriate?

I am currently collaborating with a fellow PhD student. We are both in the same Biology department, but my collaborator is more of a natural historian, so I am handling the statistical side of things. ...
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An online tree of life with extinct species present?

There are awesome online phylogenetic trees such as OneZoom. But they all only list living species. I want to see dinosaurs between birds and crocodiles. I wanna see that humans are reptiliomorphs ...
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Protein content in chemical composition of different phyla?

The protein content in the human body is roughly 15%, what are the percentages for other organisms? Bacteria, plants, fungi, protozoa, etc.
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Why would a 2019-nCoV protein sequence in the NCBI database match a protein submitted in 2018?

There seems to be a bit of a conspiracy theory brewing over some data in the NCBI database, and I don't have the necessary knowledge to make sense of it. It basically goes like this: Go to NCBI ...
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72 views

What does it mean for there to be no correlation between phylogenetic independent contrast?

I am testing the correlation between two physiological parameters in plants using the pic function in R. I am a bit stuck on the interpretation of the phylogenetic independent contrast (PIC). Without ...
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77 views

Is there any program or website that allows me to create phylogenetic trees without having to insert an already created dataset?

I asked a similar question on Quora before, but did not get any useful answers as the program the one answerer suggested turned out to have the exact same problems as all others I have found so far. ...
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What is the technical term for when a clade on a phylogenetic tree does not have an extended branch? (see image)

As we see with ZCA2, ECA2 & XCA2 these branches are compressed and do not extend as TCA does. Is there a technical term for this and what usually causes it?
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What are the methods for detecting anagenetic versus cladogenetic change?

I'm new to the study of phylogenetics and am wondering if there are ways of identifying evolutionary changes that associate with cladogenetic events versus those that arise via anagenesis.
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Phylogenical differences with nuclear and mitochondrial DNA

This is a textbook question, I would like to verify my answers. According to the textbook it is possible to construct a phylogeny using nuclear and mitochondrial DNA and these trees to be different, I ...
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280 views

Does the minimum spanning tree tell us anything useful about evolutionary ancestry?

Question migrated from bioinformatics stackexchange due to lack of interest. I'm new to bioinformatics and have been reading through a bioinformatics book, and it seems calculating a phylogenetic ...
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How to reduce the number of sequences in a Multiple Sequence Alignment?

I have a Multiple Sequence Alignment, where there are around 5000 sequences. There also exists many sequences where, there are so much of non-sequenced regions (for instance, AU----CGGGCA--NNNNNNNNNN)....
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How evolutionarily conserved are UTRs?

Coding sequences of genes have a certain degree of evolutionary conservation, so that comparisons based on sequences (BLAST, HMMER etc) can be informative. Generally speaking, the more two species are ...
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How valid is Schwartz's criticism of molecular phylogenetics?

A proponent of the human-orangutan clade, Jeffrey Schwartz argues, in this paper [1], that molecular phylogenetics is largely based on a baseless assumption. To sum up, according to him: this type of ...
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How to define ammonites?

I miss the definition of ammonite. In my opinion, many authors confuse the term "Ammonite" and "Ammonoid". Ammonoids (Ammonoidea) are large group of cephalopods including for example goniatites (...
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How to create a phylogenetic tree (using Maximum Likelihood method) in newick format for a Multiple Sequence Alignment file in FASTA format?

The file size is really big (26.7 MB). So, I am unable to use the online web tools, as they cannot handle such large input data.
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What is the best argument for maximum parsimony method in phylogenetic tree construction?

Beside the fact that maximum parsimony is computationally cheap, what other good arguments are there for it? Is there any model behind this principle? Why would one expect this principle to provide ...
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Are phylogenetic tree construction algorithms any different than general clustering algorithms?

I suspect the answer is no. But I don't know enough to be sure that that is the case. Of course phylogenetic tree construction uses biological knowledge, e.g special distance metrics, but does it ...
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Can anyone help me with these Biology evolutionary properties homework questions? [closed]

my teacher assigned these worksheet questions, they are ungraded, but he said something might come up on the test really similar to this so I really want to get all of them right. I am pretty ...
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407 views

The phylogenetic definition of the clade Dinosauria

Up until two years ago the clade of Dinosauria was defined as all the descendants of the most recent common ancestor of Triceratops and birds. From Wikipedia: Under phylogenetic nomenclature, ...
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Question regarding when it's a homoplasy in a phylogenetic tree

If you have 2 organisms that both come directly from the same common ancestor on a phylogenetic tree, and that common ancestor does not have trait "x", is it possible for both of its direct ...
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Were there any terrestrial species in the ancestry of all crustaceans?

To the exception of woodlice, Crustaceans live in aquatic (marine or freshwater) environments. Crustaceans are arthropods which is an immensely diverse taxon. Many arthropods live in terrestrial ...
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Is there a measure for degree of reticulation in a phylogenetic network?

When working with phylogenetic networks, how does one talk about reticulate (i.e., web-like) the branches are? Is there a standard measure of this?
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How to determine the number of parameters in a phylogenetic model?

I want to calculate the AIC for a phylogeny that I inferred via maximum likelihood. To calculate the AIC I need to know the number of parameters in the model. But how do I determine this?
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Have traditional categories such as phylum, class, genus, been dispensed with in modern taxonomy?

Looking through the one zoom and EOL projects I see no reference to such categories.
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Where can I find datasets containing large phylogenetic networks?

There are many datasets out there for phylogenetic trees, one can example can be found here. However, I couldn't find something for phylogenetic networks. According to Wikipedia: A phylogenetic ...
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The protostome/deuterostome distinction and why it is important

As I unerstand it, at some point an embryo develops a hole; this hole continues to punch through, and eventually makes an opening at the other side of the embryo. If the original hole becomes the ...
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347 views

Basic question about phylogenetic trees

The following is an illustration rom my book of the phylogenetic tree of 6 animal phyla (the red stuff is mine): I think what's causing some confusion is that there are no names/years at the circled ...
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What is the closest relative to odd-toed ungulate?

I have seen about 3 variation of phylogenetic tree about odd-toed ungulate and I don't know which one is really updated or outdated or which one have more backed up theory First is odd-toed ungulate ...
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The parts of the phylogenetic nomenclature that need to be "unique"

I am not quite sure I have sorted through the diversity of approaches to nomenclature, but I had a specific question to help clarify what is going on. Basically I am just wondering what needs to be ...
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Example Clade Names in PhyloCode

After looking through the PhyloCode, the only thing I found that looked like an example was in Article 9, Chapter 4: A node-based definition may be abbreviated "<A&B" or "<A&B&C&...
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What could explain discrepancies between dates provided by the fossil record vs. the molecular clock?

I am studying a mud snail genus called Ecrobia. For the Caspian species (Ecrobia grimmi), there is a discrepancy between dates provided by the fossil record and the molecular clock: First appearance ...
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Why the SNPs from the earliest human haplogroups are missing in people outside of Africa if they are infact the descendants of it?

The SNPs M91, P97, M31, P82, M23, M114, P262, M32, M59, P289, P291, P102, M13, M171, M118 from haplogroup A and SNPs M60, M181, P90 from haplogroup B are missing in people without recent African ...
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Estimating population divergence time with a single mitochondrial marker

Is it possible to estimate population divergence time with a single mitochondrial marker? Here is additional information for my specific case: Mitochondrial marker: Cytochrome Oxidase Subunit 1 (...
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How would I represent this on a cladogram?

So, right now I am making a cladogram (More of a dendrogram) for a kingdom of fictional species, and I'm not exactly sure how to represent a certain relationship. Let's say that the oldest class in ...
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Are there any open phylogenetic projects that don't require coding to make a contribution

I am stay at home learner, not pursuing education formal education and currently doing a part time job. I've however completed masters in biotechnology and I'm studying to pursue PhD in molecular ...
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MLE estimation with Mk model in ape or phangorn?

When doing MLE with the R package ape or phangorn, is it possible to set the substitution model to Mk? If so, how does one do this?

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